To investigate the connection between molecules and behavior we developed agent-based simulators (AgentCell) and  rule-based computational tools for the stochastic simulation of cellular systems NFSim (with J. Faeder, U. Pittsburgh). To extract quantitative data from experiments we developed MicrobeTracker (with C. Jacobs Wagner). NFsim and MicrobeTracker are freely available and count hundreds of users each. There is now a new version of MicrobeTracker called oufti and NFSim has been integrated into the cell simulator VCell

NFsim (The Network-Free Stochastic Simulator)
A general-purpose, open-source, biochemical reaction simulator with advanced capabilities for coarse-graining reaction mechanisms. NFsim implements a novel agent- and rule-based simulation engine that provides exact stochastic results. For many complex biological systems, NFsim provides orders of magnitude speedup over standard ODE and stochastic methods.

Links and Downloads: 

  • The NFsim web site with examples and software download
  • For beginners we recommend using the integrated framework called RuleBender that integrates a user friendly graphical interface to specify and run models with BioNetGen (rule-based language) and multiple solvers included NFsim (stochastic solver). All this resides on the BioNetGen webpage. Direct downloads to RuleBender is here.
  • NFsim user manual
  • NFsim github repository

MicrobeTracker Suite
A MATLAB-based software package designed to detect and outline bacterial cells in microscopy images and to analyze fluorescence signal inside them. The Suite consists of the MicrobeTracker program itself, which outlines and tracks the cells, a few tools for spot detection inside cells under the general name SpotFinder. See Mol. Micro., 80(3):612–627, May 2011 (pdf, html, supp. info., supp. movies, source code). A new improved version of this code has been developped under the name oufti

Agent-based simulation framework for modeling cellular behavior. See AgentCell: a digital single-cell assay for bacterial chemotaxis Bioinformatics, 1; 21(11):2714-21 (2005). (pdf, html, supp. info.) and Relationship between cellular response and behavioral variability in bacterial chemotaxis,
Proc. Natl. Acad. Sci., 105(9):3304-9(2008). (pdf, html, supp. info.).